Though I lived in Japan for more than five years, I did so as a young imbecile: I never saw Kyoto in more than a perfunctory way and when I did it was with my mother's voice in my ears. The city's temple gardens—the carefully combed pebbles, the clipped bushes, the strategic placement of every fountain, rock, tree—elicited in her the greatest indignation, as though it were not merely the expression of a gardener's vision but an attack on her own. She thought gardens should be riotous, erupting with life, untamed. Nothing brought on her full contempt like the sight of a "tortured" bonsai tree.

What you think, once you block your ears to your mother's siren opinions, allows you to discover who you are. Was I longing for a Mediterranean garden with droopy vines, rose walkways, and clouds of bougainvillea, or did I feel at home in an empty, tatami-matted tearoom, overlooking a rectangle of moss?

I went to Kyoto with my eldest brother, Giampi, who had been flown over from Belgium to advise a philanthropic foundation in Osaka. Once he had fulfilled his duties, he joined me at a beautiful old inn called Kinmata, from which we planned to investigate Kyoto's shukubos, or temple lodgings.

The first evening was the way we remembered Japan 30 years earlier: a tatami-matted room in a traditional Kyoto ryokan with only nine guest rooms; a fragrant cedarwood ofuro tub brimming with scalding hot water; a kaiseki dinner—a stately sequence of lacquered boxes and bowls—served to just the two of us, in our newly scrubbed skins, wrapped in blue-and-white cotton kimonos. Following an old complicity between us, whatever I couldn't eat, he would. Some of the combinations were surprising and delicious: fried whitebait, for instance, to be dipped in a bowl of powdered green tea and salt.

Giampi had to work in the morning, and I considered staying in my room to avoid the typhoon headed our way. The innkeeper said that by midday it would be safe to go out. (His children had yelled "Banzai!" at the news of the impending storm, since it meant they wouldn't have to go to school.) By nine, the sky had settled into a steady, uneventful rain, and I took a cab to the temple of Myoshin-ji. One feels like a large and lucky baby in a Japanese taxi, reclining against pristine white lace upholstery, with the driver wearing gray livery, a bow tie, a hat, and white gloves.

Myoshin-ji is a compound of 47 temples, of which only a fraction can be visited. Walking in from the back entrance, I was greeted on the left by a stone Buddha with a frivolous shred of pink fabric tied like a bib around its neck. Farther up was the garden of Taizo-in. I walked around a pond graced by pink water lilies and sat beneath a bamboo arbor, where I stared happily at the raindrops rippling the surface. Filtered by leaden clouds, the light turned everything an incandescent green. In the pond, an island the circumference of my arms had a sampling of moss, maple, and pine. At a wooden hut by the ticket booth, I was served a red bean cake and a bowl of foamy green tea. The screens were open and I was enveloped by the sound of rain on leaves, the fragrance of wet earth, the sight of trembling branches stirred by a light wind and rivulets of water rolling off them. In the words of the 18th-century Japanese poet and monk Ryokan, I was "alone, yet the intimate friend of a thousand green poems written on the surrounding foliage." I thought that if I had to fly home that very afternoon I wouldn't mind too much. I had found what I was searching for.

At the inn, when I looked over a list of temples willing to take in foreigners, I pictured each one more authentic than the last. I discarded one that was for women only, several others because they had a 10 p.m. curfew, any that did not have a bath on the premises. From the remaining few, I settled on the shukubo that seemed to have the most amenities. I began to imagine quiet, dusky gardens and mysterious chambers from which one might hear chanting in the early morning if one stopped turning one's head on the crackling buckwheat pillow.

This vision collided against the sight of the building our cab pulled up to that evening—a cement structure with little to recommend it aside from the view. It was up a mountain, in Higashiyama. The hostess was disheveled and disgruntled. She said we would have to make our own dinner arrangements. We looked at the many pairs of shoes at the entrance and thought she must have a full house. In fact, all the shoes belonged to her daughter, to the resident monk, and to herself. She showed us to our rooms—the kind of accommodations that are doubly frustrating because though there is nothing ostensibly amiss, one would like to leave instantly.

It was late, but we resolved that before dinner we would inspect a few other lodgings in the hope of remedying our situation. Eager to help, a taxi driver took us to a temple lodging he knew, a forbidding tall gray building with sealed-off windows, and to several others on my list. One almost impossible to pronounce, Chishakuinkaikan, made the place we had repudiated seem immensely desirable (at least its rooms had tatami mats and a view of trees).

The very next stop, however, was Myoken-ji, a temple on beautiful grounds, whitewashed and with wooden beams ornamenting its façade. It was just what we had hoped for. The high-ceilinged entrance hall was very quiet, but just past the threshold our presence set off a peal that brought a woman running. This was our first glimpse of Myajima-san, a small hunched figure in a perennial rush; she might have been 50 or 70.

Already liking the setting, we asked to see the guest rooms. At breakneck speed, shuffling in her slippers and making the floors squeak (a system devised to warn off intruders), she led us around a courtyard planted with moss and bamboo, then down a corridor past one row of sinks, and another. The place had the feel of a boarding school. There were three main pagoda-like structures. To the left, she gestured, were the communal ofuro tubs—one for men, the other for women. My heart sank a little as we descended three steps onto an AstroTurf-covered walkway leading to a humble annex. It needn't have: within were two adjoining rooms, tatami-matted and with windows overlooking a courtyard and an ideal Japanese garden. Five thousand yen, she said, including breakfast (about $44). The rooms came with no service—we would roll out our own futon from the closet at night and store it in the morning—but they were as beautiful as (and certainly more authentic than) those at Kyoto's fabled Tawara-ya Inn, at a tiny fraction of the cost. Tomorrow, we told Myajima-san, and skipped off to dinner, gloating over our good fortune.

The cement palace seemed almost cozy now that we knew we would soon abandon it, and we slept very well. On getting up, we decided to inspect the "morning prayer." When our unwilling hostess saw us heading in the direction of the prayer room, we became aware of a shuffle. If we had been hoping to see a community at prayer, we were disappointed. Soon, in the brand-new "temple," where the pillow on which the drum was propped was still wrapped in plastic, a grave-looking and rather young monk of the Shingon sect, an esoteric branch of Buddhism, made his appearance. Clothed in a diaphanous black kimono over white robes, he knelt and, banging the drum repeatedly, chanted mantras for about half an hour. It did not help our jet lag.

Entering the dining room, we mentally took back all our previous criticism of our hostess. There, on a small table, she had carefully arranged the most delectable Japanese breakfast—rice, fish, soup, and pickles. But she rushed over to shoo us away and motioned us to sit at a large table, where she eventually brought what she considered a suitable breakfast for foreigners: fried eggs with peas. The other breakfast was for the monk.

When we told her we were leaving, she became charming, even hospitable. We deduced that she, the monk, and her teenage daughter (of whom we felt we knew something, having seen all her shoes including a pair of high-heeled platform boots) had persuaded the temple treasurer to give them funds to renovate the lodgings, which they could have to themselves if only they could successfully discourage lodgers.

Giampi sweetly let me decide where to go each day. I wanted to see the gardens of Muso Soseki, the 14th-century monk, poet, and gardener. We attempted to visit his Saiho-ji, west of Kyoto, which is better known as Kokedera, or Moss Temple, because about 40 different types of moss grew there in the centuries that the garden was neglected. There was no moss at all in Soseki's time, according to a 15th-century Korean scribe, only "strange stones, weird trees, and odd flowers." The guard at the gate was adamant that we needed permission to enter. We had driven such a long way, more than an hour, that I nearly lost my temper, but my brother deployed all his diplomatic skills and we left with a signed and stamped permission slip for the following day. The garden never seemed so irresistible as in that moment when we were denied access to it.

The next day, our high expectations and the rigidity of the tour (we were forced to march up and down the paths in single file) nearly ruined it for us. I nonetheless caught a glimpse of shaded hillocks covered in thick moss and a log bridge across a narrow strait of the pond.

Nearby was the temple of Tenryu-ji and its waterless waterfall—the placement of stones gives the sense of an invisible current. This too, like Saiho-ji, was designed by Muso Soseki. In fact, the two are about half a mile apart, and he went back and forth between them, working on both at the same time. Giampi and I sat side by side in the dining hall on long red felt mats. Red lacquer trays, each filled with seven red lacquer bowls and dishes, were soon deposited in front of us. All the contents were tofu disguised as one thing or another—with the texture of chicken, beef, and eggs, in soup or gelatin—and delicious.

Unable to resist the lure of seeing more, we proceeded to Daisen-in, on the grounds of Daitoku-ji. The presiding abbot, upon finding out we were Italian, started singing "Fratelli d'Italia" at the top of his lungs. Giampi was taken with him and gave him a thousand yen for an inscription in brush and ink in the notebook he kept of temple visits, and another thousand to have a photograph taken standing next to him inside a television frame the abbot held around them. "I don't know how holy he may be," my brother said, "but he is certainly funny."

"The funnier, the holier," I said. Proving my point, the garden of the Hojo, the principal building at Daitoku-ji, consisted of two cones made of raked pebbles, looking like a pair of breasts rising serenely from an expanse of carefully raked rippled gravel. Such a simple idea, and yet it had to be maintained—hours of painstaking, backbreaking raking. That's why volunteers are welcome: the wide-eyed, floaty species of aesthete is encouraged to come to earth for a spell and be immersed in the repetition of raking.

Not until the last day did I get up in time to see the monks at morning prayer at Myoken-ji. I was surprised to find just an old priest banging a large drum and a young priest chanting from the Lotus Sutra. At a distance it had sounded like a hundred men. I preferred my own devotions, a sort of daydreaming that came over me whenever I found myself in a deserted garden with a wooden terrace on which to sit cross-legged. I don't know what pleasure has to do with faith, but I think they are threads entwined in the eye of a needle. Pleasure is an intense distraction, and Japanese gardens, especially Zen gardens, are designed as an unhurried journey from one distraction to another. Day after day, at Myoken-ji, I became lost in observing water dripping from a bamboo faucet onto a stone basin; a few branches protruding from the evenly clipped circumference of an azalea bush; pebbles lying in unmoving landscapes; pine trees extending their twisted limbs so far from their trunks that they had to be supported.

On my last day I went to Entsu-ji, a temple in the north of the city that has what the Japanese call a "borrowed view," because the garden is designed to make use of the surrounding scenery, in this case Mount Hiei. It was a cloudy day with sudden bursts of sun. A black-and-yellow dragonfly with rainbow-colored wings rested on a leaf. There were seven pines at the back of the garden, three in front of a hedge, four behind it; a stretch of bamboos; the outline of the mountain. I heard frog calls, a distant radio, a bumblebee approaching and receding, the cackling of geese, and a disembodied voice from a loudspeaker explaining the temple's origins in a low growl. The usher did not seem to find this intrusion incongruous, but he reassured me that the tape would soon be over. And it was.

The word temple is misleading—the buildings themselves are no more than shelters from which to view nature. The ones that will fill you most with wonder are those in which you are alone.

Where to Stay
For old-fashioned Japanese luxury, consider spending your first night at Kinmata inn (407 Shijo-agaru, Gokomachi, Nakagyo-ku; 81-75/221-1039; rooms from $220, including dinner). The prettiest rooms overlook the little garden, but the upstairs ones are also beautifully appointed with antique furniture and tatami mats. The famous Midori suite at Tawara-ya Inn (Anekoji-agaru, Fuyacho-dori, Nakagyo-ku; 81-75/211-5566; from $350) has a private ofuro with a floor-to-ceiling window looking out on a minute private garden (skip the new wing). Right across the street from Tawara-ya is Hiiragi-ya (Oike-kado, Fuyacho-dori, Nakagyo-ku; 81-75/221-1136; from $307), where Charlie Chaplin once stayed.
TEMPLE LODGINGS There are three interior gardens at Myoken-ji (Higashi-iru, Teranouchi, Horikawadori, Kamigyo-ku; 81-75/414-0808; $44, including breakfast)—a small bamboo court, the main garden between the two principal buildings, and a smaller one that some of the guest rooms border. The communal bathrooms feel like camp. Located near Myoken-ji, Myoren-ji (Higashi-iru, Ohmiya, Teranouchidori, Kamigyo-ku; 81-75/451-3527; $40) is evocative, but you must be prepared to use the public bath down the street. Rokuo-in (24 Kitahori-machi, Saga, Ukyo-ku; 81-75/861-1645; $40, including breakfast) is for women only.

Temple Gardens
NORTHERN KYOTO At Daitoku-ji (Daitokuji-cho Murasakino, Kita-ku; 81-75/491-0019), there are 21 temples. I recommend the rock gardens of Daisen-in (and especially the raked pebble garden that has the two breast-shaped cones). Small Entsu-ji (Hataeda-cho Iwakura, Sakyo-ku) is rarely in guidebooks.
WESTERN KYOTO Of the 47 temples at Myoshin-ji (Hanazono Myoshinji-cho, Ukyo-ku; 81-75/463-1334), only a few are open to the public. One, Taizo-in, has a beautiful garden. Visit Tenryu-ji (Saga-tenryu-ji, Susukino Babacho, Ukyo-ku; 81-75/881-1235) and the gardens by Muso Soseki. To see Saiho-ji (56 Kamigatani Matsuo, Nishigyo-ku; 81-75/391-3631), you need a permit.
SOUTHERN KYOTO At Tofuku-ji (Honmachi, Higashiyama-ku; 81-75/551-0334), the tiny garden of the Sesshu-ji subtemple is a gem.
EASTERN KYOTO Shisendo (Monguchi-cho Ichijyoji, Sakyo-ku), which means "House of Poet Hermits," has azalea bushes clipped in the shape of Mallomars. Nanzen-ji (Fukuchi-cho Nanzenji, Sakyo-ku) is worth a look for the gardens of moss and stone.

Secular Kyoto
In Nakagyo-ku, in central Kyoto, an elegant noodle restaurant, Kawamichi-ya (Sanjo-agaru, Fuyacho-dori; 81-75/221-2525; dinner for two $150), has a little room at the end of a walkway with two tiny tables and large windows overlooking gardens.
Ponto-cho is a riverside promenade that's lively at night. You'll find restaurants, pachinko and video-game halls, itinerant musicians, and very young kids on their cell phones. Here, as in Gion (the main geisha quarter), you get a very different view of Kyoto than the quiet one of temples and gardens.
The Takashimaya department store (52 Shin-cho, Shijo-dori Kawaramachi Nishi-iru, Shimogyo-ku; 81-75/221-8811) has exquisite lacquerware and pottery, as well as yukatas custom-made from a vast assortment of fabrics. The food department is an education in itself.

Avoid the Crowds
Lesser-known temples, such as Sesshu-ji, in the compound of Tofuku-ji, can be more impressive than the famous rock garden of Ryoan-ji, where there are always throngs of visitors.

On the Web
Kyoto Zen (—A view of daily life inside the temples, along with a cleverly illustrated map.

—Emily Berquist